Combining two simulation boxes with periodic boundary

LAMMPS LAMMPS Mailing List Mirror
1

Dear Lammps users,

I am running cases with two boxes reached equilibrium and then combined into one box to study the interfacial properties.
The two boxes were built with moltemplate and got good results with the NVE ensemble with periodic boundaries. Then I used read_data command to combine these two boxes.

When running the case with combined boxes, it gave the warning like the following:
WARNING: Inconsistent image flags

WARNING: Bond/angle/dihedral extent > half of periodic box length.

Then errors like the following:
ERROR on proc 0: Out of range atoms - cannot compute PPPM

Please share me some insights on this issue.

Regards,
Chen

2

when you run with periodic boundaries, atoms will get non-zero image
flags, because atoms diffuse. With a non-zero image flag, the
coordinate of the atom is still within the box (since you are now
looking at a periodic image), and you need to add "image flag times
the box length" in that direction to get the real, so-called unwrapped
position. if you change the box dimension, e.g. when merging two data
files, this implies an undesired massive displacement of all atoms
with non-zero image flags, which in turn leads to the warnings you are
seeing and like is also the cause for the unphysical behavior.

axel.